Use NGPhylogeny.fr to analyze the set of rRNA sequence provided. Describe the methods and put the .png file from your analysis into your Lab 8 .Rmd file
Align and do phylogenetic analysis off the sequences in CIPRES using MAFFT and FastTreeMP. You will need to click on Parameter Set and Save even if you don’t change the parameters. Download the fastree_result.tre to your computer. Put the resulting tree file in your .Rmd file
library(tidyverse)
library(ggtree)
tree <- read.tree("./data/lab-8-data/TOL_fastree_result.tre")
tree
##
## Phylogenetic tree with 21 tips and 19 internal nodes.
##
## Tip labels:
## Archaeoglobus_fulgidus, Trypanosoma_cruzi_nuclear, Amphidinium_carterae, Saccharomyces_cerevisiae_nuclear, Homo_sapies_nuclear, Drosophila_yakuba_nuclear, ...
## Node labels:
## , 0.999, 0.893, 1.000, 0.988, 0.982, ...
##
## Unrooted; includes branch lengths.
ggtree(tree) +
theme_tree2() +
geom_tiplab() +
xlim(0,2)
## Warning: `data_frame()` is deprecated as of tibble 1.1.0.
## Please use `tibble()` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_warnings()` to see where this warning was generated.
## Warning: `mutate_()` is deprecated as of dplyr 0.7.0.
## Please use `mutate()` instead.
## See vignette('programming') for more help
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_warnings()` to see where this warning was generated.
Go through the tutorial on Visualizing and Annotating Phylogenetic Trees with R+ggtree adding the steps to your .Rmd file.
library(tidyverse)
library(ggtree)
tree <- read.tree("./data/lab-8-data/tree_newick.nwk")
tree
##
## Phylogenetic tree with 13 tips and 12 internal nodes.
##
## Tip labels:
## A, B, C, D, E, F, ...
##
## Rooted; includes branch lengths.
# build a ggplot with a geom_tree
ggplot(tree) +
geom_tree() +
theme_tree()
# This is convenient shorthand
ggtree(tree)
# add a scale
ggtree(tree) +
geom_treescale()
# or add the entire scale to the x axis with theme_tree2()
ggtree(tree) +
theme_tree2()
ggtree(tree, branch.length="none")
ggtree(tree, branch.length="none", color="blue", size=2, linetype=3)
ggtree(tree, layout="slanted")
ggtree(tree, layout="circular")
ggtree(tree, layout="circular", color="red", size=2)
# create the basic plot
p <- ggtree(tree)
# add node points
p + geom_nodepoint()
# add tip points
p + geom_tippoint()
# Label the tips
p + geom_tiplab()
ggtree(tree) +
geom_tippoint(fill="purple", shape=23) +
geom_nodepoint(color="yellow", alpha=0.8, size=4) +
ggtitle("Aesthetically-pleasing phylogenetic tree")
ggtree(tree) +
geom_text(aes(label=node), hjust=-.3)
ggtree(tree) +
geom_tiplab()
MRCA(tree, "C", "E")
## [1] 17
MRCA(tree, "G", "H")
## [1] 21
ggtree(tree) +
geom_cladelabel(node=17, label="Some random clade", color="red")
ggtree(tree) +
geom_tiplab() +
geom_cladelabel(node=17, label="Some random clade",
color="red2", offset=.8)
ggtree(tree) +
geom_tiplab() +
geom_cladelabel(node=17, label="Some random clade",
color="red2", offset=.8) +
geom_cladelabel(node=21, label="A different clade",
color="blue", offset=.8)
ggtree(tree) +
geom_tiplab() +
geom_cladelabel(node=17, label="Some random clade",
color="red2", offset=.8, align=TRUE) +
geom_cladelabel(node=21, label="A different clade",
color="blue", offset=.8, align=TRUE) +
theme_tree2() +
xlim(0, 70) +
theme_tree()
ggtree(tree) +
geom_tiplab() +
geom_hilight(node=17, fill="gold") +
geom_hilight(node=21, fill="purple")
ggtree(tree) +
geom_tiplab() +
geom_taxalink("E", "H", color="blue3") +
geom_taxalink("C", "G", color="orange2", curvature=-.9)
MRCA(tree, "B", "C")
## [1] 19
MRCA(tree, "L", "J")
## [1] 23
ggtree(tree)
ggtree(tree) +
geom_tiplab()
ggtree(tree) +
geom_tiplab() +
geom_hilight(node=19, fill="purple") +
geom_hilight(node=23, fill="gold")
ggtree(tree) +
geom_tiplab() +
geom_hilight(node=19, fill="purple") +
geom_hilight(node=23, fill="gold") +
geom_cladelabel(node=17, label="Clade 17",
color="red2", offset=.8, align=TRUE) +
theme_tree2() +
xlim(0, 70) +
theme_tree()
ggtree(tree) +
geom_tiplab() +
geom_hilight(node=19, fill="purple") +
geom_hilight(node=23, fill="gold") +
geom_cladelabel(node=17, label="Clade 17",
color="red2", offset=.8, align=TRUE) +
theme_tree2() +
xlim(0, 70) +
theme_tree() +
geom_taxalink("C", "E", color="gray", linetype=2) +
geom_taxalink("G", "J", color="gray", linetype=2)
ggtree(tree) +
geom_tiplab() +
geom_hilight(node=19, fill="purple") +
geom_hilight(node=23, fill="gold") +
geom_cladelabel(node=17, label="Clade 17",
color="red2", offset=.8, align=TRUE) +
theme_tree2() +
xlim(0, 70) +
theme_tree() +
geom_taxalink("C", "E", color="gray", linetype=2) +
geom_taxalink("G", "J", color="gray", linetype=2) +
theme_tree2()
ggtree(tree) +
geom_tiplab() +
geom_hilight(node=19, fill="purple") +
geom_hilight(node=23, fill="gold") +
geom_cladelabel(node=17, label="Clade 17",
color="red2", offset=.8, align=TRUE) +
theme_tree2() +
xlim(0, 70) +
theme_tree() +
geom_taxalink("C", "E", color="gray", linetype=2) +
geom_taxalink("G", "J", color="gray", linetype=2) +
theme_tree2() +
ggtitle("Exercise 3")
ggtree(tree, layout="circular") +
geom_tiplab() +
geom_hilight(node=19, fill="purple") +
geom_hilight(node=23, fill="gold") +
geom_cladelabel(node=17, label="Clade 17",
color="red2", offset=.8, align=TRUE) +
theme_tree2() +
xlim(0, 70) +
theme_tree() +
theme_tree2() +
ggtitle("Exercise 3")
library(treeio)
# Read the data
tree <- read.beast("./data/lab-8-data/flu_tree_beast.tree")
# supply a most recent sampling date so you get the dates
# and add a scale bar
ggtree(tree, mrsd="2013-01-01") +
theme_tree2()
# Finally, add tip labels and adjust axis
ggtree(tree, mrsd="2013-01-01") +
theme_tree2() +
geom_tiplab(align=TRUE, linesize=.5) +
xlim(1990, 2020)
msaplot(p=ggtree(tree), fasta="./data/lab-8-data/flu_aasequence.fasta", window=c(150, 175))
msaplot(p=ggtree(tree), fasta="./data/lab-8-data/flu_aasequence.fasta", window=c(150, 175)) +
coord_polar(theta="y")
set.seed(42)
trees <- lapply(rep(c(10, 25, 50, 100), 3), rtree)
class(trees) <- "multiPhylo"
ggtree(trees) + facet_wrap(~.id, scale="free", ncol=4) + ggtitle("Many trees. Such phylogenetics. Wow.")
# Generate a random tree with 30 tips
tree <- rtree(30)
# Make the original plot
p <- ggtree(tree)
# generate some random values for each tip label in the data
d1 <- data.frame(id=tree$tip.label, val=rnorm(30, sd=3))
# Make a second plot with the original, naming the new plot "dot",
# using the data you just created, with a point geom.
p2 <- facet_plot(p, panel="dot", data=d1, geom=geom_point, aes(x=val), color='red3')
# Make some more data with another random value.
d2 <- data.frame(id=tree$tip.label, value = abs(rnorm(30, mean=100, sd=50)))
# Now add to that second plot, this time using the new d2 data above,
# This time showing a bar segment, size 3, colored blue.
p3 <- facet_plot(p2, panel='bar', data=d2, geom=geom_segment,
aes(x=0, xend=value, y=y, yend=y), size=3, color='blue4')
# Show all three plots with a scale
p3 + theme_tree2()
newick <- "((Pongo_abelii,(Gorilla_gorilla_gorilla,(Pan_paniscus,Pan_troglodytes)Pan,Homo_sapiens)Homininae)Hominidae,Nomascus_leucogenys)Hominoidea;"
tree <- read.tree(text=newick)
d <- ggimage::phylopic_uid(tree$tip.label)
d$body_mass = c(52, 114, 47, 45, 58, 6)
p <- ggtree(tree) %<+% d +
geom_tiplab(aes(image=uid, colour=body_mass), geom="phylopic", offset=2.5) +
geom_tiplab(aes(label=label), offset = .2) + xlim(NA, 7) +
scale_color_viridis_c()
## Loading required package: ggimage
p
Upload your tree file from the FastTreeMP output on CIPRES. Color the tree according to the domains of life. Upload a circular version of the tree to your notebook.
library(tidyverse)
library(ggtree)
tree <- read.tree("./data/lab-8-data/TOL_fastree_result.tre")
tree
##
## Phylogenetic tree with 21 tips and 19 internal nodes.
##
## Tip labels:
## Archaeoglobus_fulgidus, Trypanosoma_cruzi_nuclear, Amphidinium_carterae, Saccharomyces_cerevisiae_nuclear, Homo_sapies_nuclear, Drosophila_yakuba_nuclear, ...
## Node labels:
## , 0.999, 0.893, 1.000, 0.988, 0.982, ...
##
## Unrooted; includes branch lengths.
ggtree(tree) +
theme_tree2() +
geom_tiplab() +
xlim(0,2) +
geom_nodelab()
MRCA(tree, "Oryza_mitochondrion", "Thermotoga_lettingae_")
## [1] 30
MRCA(tree, "Drosophila_yakuba_nuclear", "Trypanosoma_cruzi_nuclear")
## [1] 25
MRCA(tree, "Candidatus_Korarchaeum_cryptofilum_", "Archaeoglobus_fulgidus")
## [1] 22
ggtree(tree, layout="circular") +
theme_tree2() +
geom_tiplab(hjust=-.1, size = 3) +
xlim(0, 2) +
geom_nodelab() +
geom_hilight(node=22, fill="green") +
geom_hilight(node=30, fill="gold", extend=0.23) +
geom_hilight(node=25, fill="purple")